A global profile of gene promoter methylation in treatment-naïve urothelial cancer

Abstract

The epigenetic alteration of aberrant hypermethylation in the promoter CpG island of a gene is associated with repression of transcription. In neoplastic cells, aberrant hypermethylation is well described as a mechanism of allele inactivation of particular genes with a tumor suppressor function. To investigate the role of aberrant hypermethylation in the biology and progression of urothelial cancer, we examined 101 urothelial (transitional cell) carcinomas (UC), broadly representative of the disease at presentation, with no prior immunotherapy, chemotherapy or radiotherapy, by Infinium HM27 containing 14,495 genes. The genome-wide signature of aberrant promoter hypermethylation in UC consisted of 729 genes significant by a Wilcoxon test, hypermethylated in a CpG island within 1 kb of the transcriptional start site and unmethylated in normal urothelium from aged individuals. We examined differences in gene methylation between the two main groups of UC: the 75% that are superficial, which often recur but rarely progress, and the 25% with muscle invasion and poor prognosis. We further examined pairwise comparisons of the pathologic subgroups of high or low grade, invasive or non-invasive (pTa), and high grade superficial or low grade superficial UC. Pathways analysis indicated over-representation of genes involved in cell adhesion or metabolism in muscle-invasive UC. Notably, the TET2 epigenetic regulator was one of only two genes more frequently methylated in superficial tumors and the sole gene in low grade UC. Other chromatin remodeling genes, MLL3 and ACTL6B, also showed aberrant hypermethylation. The Infinium methylation value for representative genes was verified by pyrosequencing. An available mRNA expression data set indicated many of the hypermethylated genes of interest to be downregulated in UC. Unsupervised clustering of the most differentially methylated genes distinguished muscle invasive from superficial UC. After filtering, cluster analysis showed a CpG Island Methylator Phenotype (CIMP)-like pattern of widespread methylation in 11 (11%) tumors. Nine of these 11 tumors had hypermethylation of TET2. Our analysis provides a basis for further studies of hypermethylation in the development and progression of UC.

936 Quantitative genome-wide methylation analysis of high-grade non-muscle invasive bladder cancer

“…However, and despite the absence of genes as being exclusively associated with either high-or low-intermediate-grade tumors, the frequency and mean levels of gene-promoter methylation in the high-grade tumors were significantly higher than in the low-intermediate-grade tumors. Indeed, similar observations with respect to differences in the frequencies of methylation between high-and low-grade bladder tumors were first suggested by Ibragimova et al 47 Similar subtype and/or grade-associated differences have been reported in other tumor types including, pituitary, breast, and colon cancer subtypes. 37,48,49 In our analysis of NMIBC it remains unclear whether the increase in frequency and/or mean levels of methylation in the more aggressive tumors represents a more rapid accumulation of epigenetic changes during tumor progression, or reflects distinct epigenetic pathways of tumor development and outgrowth.…”

“…In these cases, we identified significant over-representation of genes in processes and pathways previously reported by other groups as subject to epigenetically mediated dysregulation in tumor development. For example, these included transcription and cell signaling and adhesion, [45][46][47] suggesting possible similar roles in high-grade bladder tumors, and their validity as targets for further investigation.…”

“…In this case, normal bladder was used as control for consistency with previous array analyses, 35,47,65 and also to permit comparisons with earlier reports of non-muscle invasive bladder cancer. Arrays were processed according to the manufacturer's instructions (performed by Barts and the London Genome Center, UK), as described by us previously.…”

Framework for the Integration of Genomics, Epigenomics and Transcriptomics in Complex Diseases

“…This SNP has been positively associated with the expression of SETBP1, coding for an important cancer gene located on chromosome 18 that is observed also as a predominant hotspot in figure 3 c. Somatic mutations in SETBP1 [44] , as well as its expression patterns [45] , are related with myeloid leukaemia disease. Moreover in figure 3 b, we observed a very predominant hotspot regarding three CpGs belonging to three different genes but all closely located on chromosome 6; Two of them (cg02622316 located on gene ZNF96 and cg02599464 located on gene HIST1H41 ) have already been published as hypermethylated in individuals with muscle-invasive bladder cancer [46] . The first one is positively associated with many SNPs and gene expression probes, and the second is positively and negatively associated with some SNPs and only positively with some gene expression probes.…”

Methylation status as a predictor of intravesical Bacillus Calmette-Guérin (BCG) immunotherapy response of high grade non-muscle invasive bladder tumor

“…Studies have shown that methylation status plays an important role in carcinogenesis in various organs, including NMIBC (ref. [21][22][23][24][25][26][27][28][29][30] ). Methylation status is a potent indicator for distinguishing patients responding to BCG from those who are failing to do so and who need the radical therapy approach 31,32 .…”